Only clear wedge bond flags after normalization #163
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manuelschwarze approved these changes Jul 22, 2025
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The KNIME RDKit mol renderer currently is affected by a bug which causes cis/trans double bonds to lose their stereochemistry specification after coordinates are added. This happens because the SWIG version of
ClearSingleBondDirFlags()does not expose theonlyWedgeFlagsas the C++ version does.This PR fixes that bug by reimplementing
clearSingleBondDirFlags()in Java such that updating RDKit binaries is not required. This can be done at a later stage; I have added a comment to remind myself to remove the Java implementation ofclearSingleBondDirFlags()and switch to the C++ version instead.